摘要
基于全长转录组测序(isoform sequencing, Iso-Seq)技术对野生马齿苋叶片(对照、干旱和低温胁迫3种处理的叶片)转录组进行测序及其转录组信息分析的结果显示,总共得到641 732条原始片段,质控后得到合格的插入片段26 758 071条,总碱基量为44 Gb,利用CCS软件获得442 760条一致性序列,根据smrtlink软件得到全长的插入片段和全长的去除嵌合体的插入片段分别为391 258条和301 412条,去除冗余得到103 298条转录本,最终得到39 717条unigene,预测出40 952条LncRNA和38 419条CDS序列;并将unigene与Uniprot、Pfam、GO、KEGG、eggNOG、Pathway和Nr等数据库进行同源比对,其中36 381条unigene被注释,从这些unigene里查找到25 898个简单重复序列标记(simple sequence repeats, SSR)位点。利用差异表达分析软件DESeq2筛选不同处理组间的差异表达基因,对照和干旱处理、对照和低温胁迫处理及干旱和低温胁迫处理间分别鉴定出16 194(上调和下调差异基因分别为2 874和13 320)、16 093(上调和下调差异基因分别为6 365和9 728)和25 498(上调和下调差异基因分别为15 163和10 335)个差异表达基因。研究结果可为马齿苋属植物基因研究和SSR开发研究提供参考。
The transcriptome of wild Portulaca oleracea’s leaves(leaves of three treatments: control, drought stress and low temperature stress) was sequenced and analyzed by Iso-Seq technology. The results showed that 641 732 polymerase reads were generated from the transcriptome of P. oleracea’s leaves. 26 758 071 subreads and 44 Gb total bases were obtained by quality control methods. 442 760 consensus sequences were generated by using CCS software. 391 258 full-length reads and 301 412 full-length non-chimeric reads were generated based on Smrtlink software. 103 298 transcripts were obtained from these consensus sequences by removing redundancy, and 39 717 unigenes were generated from these transcripts by removing redundancy. 40 952 LncRNAs and 38 419 CDS sequences were predicted from the unigenes. Unigenes were aligned to the sequences of public databases, including UniProt, Pfam, GO, KEGG, eggNOG, pathway and NR databases, in which 36 381 unigenes were annotated, and 25 898(simple sequence repeats) SSR loci were detected in the unigenes. The differentially expressed genes(DEGs) among different treatment groups were screened by using DESeq 2.16 194(Up: 2 874, Down: 13 320), 16 093(Up: 6 365, Down: 9 728) and 25 498(Up: 15 163, Down: 10 335) DEGs were obtained in C vs DS, C vs LTS, and DS vs LTS, respectively. This study could provide reference for gene research and SSR development of P. oleracea.
作者
叶梅荣
黄守程
王晓鹏
刘爱荣
崔峰
康健
YE Meirong;HUANG Shoucheng;WANG Xiaopeng;LIU Airong;CUI Feng;KANG Jian(College of Life and Health Sciences,Anhui Science and Technology University,Fengyan 233100,Anhui,China)
出处
《浙江农业学报》
CSCD
北大核心
2023年第1期67-78,共12页
Acta Agriculturae Zhejiangensis
基金
安徽科技学院稳定人才项目(SKWD201601)
安徽科技学院创业创新项目(X202110879017)
安徽省自然科学基金(1808085MC78)
安徽省创新训练项目(S202110879058,S202110879059)。
关键词
马齿苋
转录组
Iso-Seq技术
Portulaca oleracea L.
transcriptome
Iso-Seq technology
